Sam file is empty afertern aligned reads?

[ChengYunazhi]

Hi, @khuang28jhu

when snap aligning reads, everthing seems ok, as below:

as you can see, the align ratio for reads input is high, but the sam file is empty, there is no aligned reads, so the methylation information is empty too:

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[khuang28jhu]

Can you give me more context? The commands you used, the genome you matched to...etc

and whether you tried the example test case and if it worked

and your version of gcc

[ChengYunazhi]

@khuang28jhu I tried test data, it works and get the results

genome: ~440MB with 15 chromosome Reads: PE150

command for generate index:

/DataProcess/softwares/bs3-dev1/bs3-build.py -s 23 -f /DataProcess/Resource/genomes/genome.fa

command for align:

./bs3-align.py -1 /cleandata/B.1.fq.gz -2 cleandata/B.2.fq.gz -o B -f sam -g genome.fa -d bs_seeker3_index/reference_genome --temp_dir /DataProcess/tmp

[khuang28jhu]

Would you mind sharing with me the data you are using, because I can not reproduce the error with the command you are using on my test data.

[SchulzLab]

Hi, I have the same problem. A lot of SNAP jobs are running but at the end no alignment. I noticed in the error log that I made that SNAP reports the following error: Welcome to SNAP version 1.0beta.23.

Unmatched read IDs 'SRR4238609.21452285.1' and 'SRR4238609.21452285.2'. Use the -I option to ignore this. SNAP exited with exit code 1 from line 47 of file SNAPLib/Read.cpp

This error occurred 137 times while running bseeker3. Could it be that some of the default SNAP parametrisation in the current GitHub version is messed up? Maybe it has to do with the type of paired-end library? Anyway right now I am stuck.

Regards, Marcel

[lihui215]

I have the same qutions, and how to fix it? @khuang28jhu